The station opened as the southern terminus of the original Yonge subway line on March 30, 1954.

On February 28, 1963, Union became a through station with the opening of the University section of the Yonge–University line.

On June 22, 1990, Union became the underground terminus of the former 604 Harbourfront LRT, now served by the 509 Harbourfront and 510 Spadina routes. Both Spadina and St. Clair West stations were designed with an underground streetcar connection in mind. Retrofitting Union Station required building a pedestrian tunnel approximately 30 metres long, with a flight of stairs in the middle leading from the station's mezzanine level.[3]

In 1996, elevators became operational and it was one of the first accessible subway stations.[4] There was even an elevator added in the streetcar access corridor from the mezzanine level even through accessible streetcars were still years away.[3]

By 2011, often no transfer was required to transfer to or from a streetcar in the underground loop to the main subway system. However, some summers tourists were allowed to board streetcars along Queens Quay without paying a fare. During these times passengers alighting at Union Station were asked to either pay a fare or show a valid transfer.[5] The introduction of proof-of-payment on the 509 and 510 routes eliminates this practice.

On August 18, 2014, the TTC opened the second platform for Yonge-bound trains.[6]

Union’s status as a transport hub has resulted in overcrowding on its narrow centre platform, often requiring TTC personnel to regulate the number of passengers allowed to wait on the platform at a given time. This results in overcrowding in the concourse level and significant commuter delays.

In 2003, public consultations and planning meetings were held to examine options to reduce crowding in the station. The resulting plan calls for the current platform to be re-purposed to serve only the University line trains, while a new platform would be built on the south side of the existing tracks to serve the Yonge line trains. Preparatory construction for the expansion (mainly re-locating utilities buried in the area to be excavated for the new platform) began in 2006. The project went to public tender in April 2010 and construction commenced in February 2011.[6] The second platform opened on August 18, 2014.[10] A new level access corridor was built between the new subway platform (for Yonge-bound trains) and the streetcar loop eliminating the stairs and elevator of the old corridor.[3]

Panel from Zones of Immersion by Stuart Reid opposite the new platform

When the subway opened in 1954, this station had glossy Vitrolite tiles, using yellow background tiles and red lettering and trim. The station name on the walls was the TTC’s unique Gill Sans-inspired subway font. During renovations in the 1980s, the yellow vitrolite tiles were replaced with brown ceramic tiles and vinyl siding and the station font became Univers. With the second platform renovation, grey tiles were used and the UNION station name returned to its original subway font.[3]

As part of the second platform project, a glass wall has been built to block off the southern side of the old platform since it now only serves the University line. On this wall, Stuart Reid has created the art work "Zones of Immersion".[11] The work comprises 166 large glass panels, each measuring more than one by two metres, extending 170-metre (560 ft) along the length of the platform. Mostly transparent, it is visible from both the Yonge and University platforms. Each panel contains images or words, many based on sketches that Reid drew while riding the subway. Reid is a professor at the Ontario College of Art and Design University and a stained-glass artist.[12]

Leaving the station eastbound, the Yonge leg of the line runs briefly under Front Street and turns 90 degrees north to run under Yonge Street; leaving westbound, the University leg also runs under Front Street, and eventually turns 90 degrees north to run under University Avenue.

This station is one of the only stations that has a curved platform (the other one being St Clair station).

The station is also noted as being one of only three stations on the TTC where a signal light is publicly accessible (the others being Davisville and Islington Station). The signal is located on the east (trailing) end of the University line platform. It is an interlocking signal that protects the crossover to the northbound Yonge Line and is only occasionally used to reverse Yonge Line trains at Union.[3]

^"Subway ridership, 2012-2013"(PDF). Toronto Transit Commission. This table shows the typical number of customer-trips made on each subway on an average weekday and the typical number of customers travelling to and from each station platform on an average weekday. Five stations serve two subways, and so are listed twice, once for each subway

^"Wi-fi Now Available At". TCONNECT. Retrieved January 2015. Each of the 65 underground stations will have wireless and Wi-Fi service by 2017

^Nick Westoll (August 17, 2014). "TTC opens Union Subway Station second platform". Retrieved August 2014. The TTC will also be installing a 500-foot glass art wall to block off the southern side of the University line platform. Stuart Reid won an international public art competition for his piece, “Zones of Immersion,” in 2012.